I got some rather complex movements in a scene, so I use a lot of parenting chains to keep track of my planned movements.
So, I am not parenting and/or unparenting now that I'm almost done.
But when I try to adjust the animation of certain nulls and objects, I can't do a full undo.
Somehow part of the adjustment is now baked into the child's behavior. I can imagine this will happen if you unparent and parent when animating. That can cause big problems but I avoided that.
I did find out it gets more evil when you combine 2D and 3D in one scene. Keeping everything 3D is best.
Some problems were fixed when I made assets 3D and tried to adjust again.
The After Effects CC 2015 (13.6.1) bug-fix update is available. It fixes several bugs, including one that sounds related to your issue.
Let us know how things work after you have installed the update.